Table 3 Evaluation of submitted gene sets.
From: nGASP – the nematode genome annotation assessment project
Gene set | Category | Base | Exon | Isoform | Gene | ||||
|---|---|---|---|---|---|---|---|---|---|
Sn | Sp | Sn | Sp | Sn | Sp | Sn | Sp | ||
Agene | 1 | 93.8 | 83.4 | 68.9 | 61.1 | 9.8 | 13.1 | 12.0 | 14.1 |
AUGUSTUS v1 | 1 | 97.0 | 89.0 | 86.1 | 72.6 | 50.1 | 28.7 | 61.1 | 38.4 |
AUGUSTUS v2 | 1 | 96.8 | 89.3 | 84.8 | 74.3 | 49.3 | 31.9 | 60.5 | 32.7 |
CRAIG | 1 | 95.6 | 90.9 | 80.2 | 78.2 | 35.7 | 36.3 | 43.8 | 37.8 |
EUGENE | 1 | 94.0 | 89.5 | 80.3 | 73.0 | 49.1 | 28.8 | 60.2 | 30.2 |
ExonHunter | 1 | 95.4 | 86.0 | 72.6 | 62.5 | 15.5 | 18.6 | 19.1 | 19.2 |
Fgenesh | 1 | 98.2 | 87.1 | 86.4 | 73.6 | 47.1 | 34.6 | 57.8 | 35.4 |
GeneID | 1 | 93.9 | 88.2 | 77.0 | 68.6 | 36.2 | 22.8 | 44.4 | 25.1 |
GeneMark.hmm | 1 | 98.3 | 83.1 | 83.2 | 65.6 | 37.7 | 24.0 | 46.3 | 24.5 |
GlimmerHMM | 1 | 97.6 | 87.6 | 84.4 | 71.4 | 47.3 | 29.3 | 58.0 | 30.6 |
MGENE v1 | 1 | 97.2 | 91.5 | 84.6 | 78.6 | 44.6 | 40.9 | 54.8 | 42.3 |
MGENE v2 | 1 | 96.9 | 91.6 | 84.2 | 78.7 | 44.0 | 40.9 | 54.0 | 42.4 |
MGENE v3 | 1 | 96.9 | 91.6 | 84.2 | 78.6 | 43.5 | 40.5 | 53.4 | 44.8 |
SNAP | 1 | 94.0 | 84.5 | 74.6 | 61.3 | 32.6 | 18.6 | 40.0 | 19.1 |
EUGENE | 2 | 96.2 | 87.5 | 82.8 | 72.8 | 50.3 | 30.2 | 61.7 | 31.4 |
MGENE v1 | 2 | 97.7 | 90.9 | 85.8 | 78.4 | 51.6 | 41.2 | 63.3 | 42.5 |
MGENE v2 | 2 | 97.7 | 90.9 | 85.8 | 78.3 | 51.2 | 40.9 | 62.7 | 43.8 |
N-SCAN | 2 | 97.4 | 88.1 | 83.5 | 70.8 | 39.2 | 27.7 | 48.1 | 28.4 |
SGP2 | 2 | 93.5 | 90.0 | 77.3 | 70.3 | 36.4 | 24.9 | 44.6 | 27.1 |
AUGUSTUS v1 | 3 | 99.0 | 90.5 | 92.5 | 80.2 | 68.3 | 47.1 | 80.1 | 51.8 |
EUGENE v1 | 3 | 97.3 | 85.3 | 88.5 | 72.2 | 55.7 | 33.7 | 68.4 | 34.2 |
EUGENE v2 | 3 | 98.5 | 85.1 | 92.1 | 70.3 | 60.8 | 31.5 | 68.8 | 36.1 |
ExonHunter v1 | 3 | 97.6 | 87.3 | 83.9 | 69.3 | 38.5 | 31.9 | 47.3 | 32.5 |
ExonHunter v2 | 3 | 93.7 | 92.0 | 81.2 | 76.9 | 37.2 | 39.7 | 45.6 | 40.5 |
Fgenesh++ | 3 | 97.6 | 89.7 | 90.4 | 80.9 | 65.5 | 53.4 | 78.3 | 54.2 |
Gramene v11 | 3 | 98.2 | 95.4 | 88.5 | 71.8 | 41.7 | 19.6 | 48.7 | 37.2 |
Gramene v21 | 3 | 98.6 | 94.8 | 88.3 | 67.8 | 38.7 | 16.3 | 46.0 | 39.0 |
MAKER (using SNAP) v1 | 3 | 92.9 | 88.5 | 80.7 | 66.3 | 41.3 | 19.6 | 50.7 | 47.6 |
MAKER (using SNAP) v2 | 3 | 92.6 | 91.1 | 80.5 | 69.5 | 40.8 | 23.2 | 50.1 | 28.0 |
MGENE v1 | 3 | 98.7 | 91.9 | 91.0 | 80.7 | 57.7 | 48.0 | 70.8 | 48.9 |
MGENE v2 | 3 | 98.9 | 87.9 | 91.9 | 75.9 | 62.6 | 38.7 | 76.9 | 39.5 |
MGENE v3 | 3 | 98.7 | 91.9 | 91.0 | 80.6 | 57.7 | 48.0 | 70.6 | 51.1 |
EUGENE v1 | 4 | 98.5 | 85.6 | 90.5 | 75.1 | 60.4 | 39.3 | 75.9 | 39.5 |
EUGENE v2 | 4 | 99.4 | 85.4 | 94.3 | 72.6 | 63.9 | 35.9 | 74.7 | 42.0 |
EUGENE v3 | 4 | 98.6 | 85.6 | 90.6 | 74.2 | 63.3 | 36.9 | 79.5 | 37.4 |
EUGENE v4 | 4 | 99.2 | 85.3 | 94.0 | 71.8 | 67.1 | 33.9 | 77.9 | 39.8 |
Evigan | 4 | 99.3 | 89.6 | 91.1 | 82.3 | 64.2 | 52.4 | 80.7 | 52.7 |
Fgenesh++C | 4 | 98.7 | 89.7 | 91.1 | 82.7 | 66.1 | 56.3 | 80.3 | 57.1 |
GeneID v1 | 4 | 99.3 | 91.5 | 93.0 | 83.8 | 63.9 | 53.3 | 78.3 | 57.7 |
GeneID v2 | 4 | 99.0 | 92.0 | 90.7 | 85.0 | 61.7 | 55.5 | 77.5 | 57.1 |
GENOMIX v1 | 4 | 97.1 | 88.6 | 86.2 | 77.4 | 52.4 | 39.0 | 65.9 | 42.2 |
GENOMIX v2 | 4 | 98.1 | 90.4 | 89.7 | 83.5 | 60.4 | 53.3 | 75.9 | 56.1 |
GESECA | 4 | 98.8 | 82.8 | 87.6 | 66.8 | 45.1 | 25.9 | 52.6 | 27.4 |
GLEAN | 4 | 98.9 | 87.3 | 88.3 | 75.4 | 51.4 | 37.0 | 64.7 | 37.6 |
Gramene1 | 4 | 97.5 | 80.9 | 82.7 | 48.7 | 22.4 | 6.1 | 27.3 | 30.3 |
JIGSAW v1 | 4 | 98.9 | 93.2 | 90.5 | 87.4 | 63.6 | 60.2 | 79.9 | 61.0 |
JIGSAW v2 | 4 | 98.9 | 91.7 | 89.9 | 83.0 | 62.0 | 51.1 | 77.9 | 52.0 |